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From: Charly B. <cha...@gm...> - 2013-10-08 14:28:44
|
Hello all, Could you pls advise? I am a Webapollo user. At the moment, I am looking for a way to delete a particular scaffold either from the web browser or straight from the server. Also, is it possible to import multiple scaffold at the same time? I am trying to modify setup_webapollo to achieve this but I ran into trouble with the way the whole process is configured (from GFF file to database) ...keep complaining of duplicate. Thank you, Charly |
From: Faino, L. <lui...@wu...> - 2013-08-25 07:33:00
|
Dear all, I need to load a bam file in web Apollo. Actually I can load the file by using bam to json but the way that is displayed is not good. On the other hand when I load the file via open option in the jbrowse visual interface it displays very well showing introns and matching part. How can I use the setting of the open in the interface and pass to the bam to json? Thanks in advance Luigi Inviato da iPad |
From: Zafar, N. <nz...@jc...> - 2013-03-01 20:20:55
|
Hi, I followed the directions given on this page http://www.gmod.org/wiki/WebApollo_Tutorial_2012#Installing_WebApollo to configure and setup the tracks for the test data, but when I click on the edit button selectTrack.jsp page is empty. I checked the logs and could not find any error and browsers error console show this message : Timestamp: 03/01/2013 02:54:28 PM Error: ReferenceError: trackName is not defined /servlet/selectTrack.jsp Line: 81 Can somebody tell me what might be going on. Thanks a lot, Nikhat |
From: <gk...@us...> - 2013-02-08 21:25:43
|
Revision: 25282 http://gmod.svn.sourceforge.net/gmod/?rev=25282&view=rev Author: gk_fan Date: 2013-02-08 21:25:30 +0000 (Fri, 08 Feb 2013) Log Message: ----------- Relaxed URL encoding since current qBlast service doesn't handle certain escape codes. Modified Paths: -------------- apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java Modified: apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java =================================================================== --- apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java 2013-02-01 21:04:39 UTC (rev 25281) +++ apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java 2013-02-08 21:25:30 UTC (rev 25282) @@ -361,7 +361,7 @@ if (opts.isSetFilterMaskLookup()) { buf.append("FILTER=m&"); } - buf.append(URLEncoder.encode("GAPCOSTS=" + opts.getGapOpenCost() + " " + opts.getGapExtendCost() + "&", ENCODING)); + buf.append("GAPCOSTS=" + URLEncoder.encode(opts.getGapOpenCost() + " " + opts.getGapExtendCost(), ENCODING) + "&"); buf.append("GENETIC_CODE=" + opts.getGeneticCode() + "&"); buf.append("HITLIST_SIZE=" + opts.getNumberOfHits() + "&"); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2012-11-08 09:48:25
|
Revision: 25276 http://gmod.svn.sourceforge.net/gmod/?rev=25276&view=rev Author: gk_fan Date: 2012-11-08 09:48:15 +0000 (Thu, 08 Nov 2012) Log Message: ----------- Fixed casting issue for ChadoProgram arrays that was causing a ClassCastException. Modified Paths: -------------- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java Modified: apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java 2012-10-12 20:48:34 UTC (rev 25275) +++ apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java 2012-11-08 09:48:15 UTC (rev 25276) @@ -106,7 +106,7 @@ return null; } else { - ChadoProgram [] cdsChadoPrograms = (ChadoProgram [])cdsChadoPrgs.toArray(); + ChadoProgram [] cdsChadoPrograms = (ChadoProgram [])cdsChadoPrgs.toArray(new ChadoProgram[0]); analysisWhereStr.append("AND cds.feature_id = af.feature_id "); // analysis table is cached; no need to add it to the query This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2012-10-12 20:48:42
|
Revision: 25275 http://gmod.svn.sourceforge.net/gmod/?rev=25275&view=rev Author: gk_fan Date: 2012-10-12 20:48:34 +0000 (Fri, 12 Oct 2012) Log Message: ----------- Updated version to 1.11.7 Modified Paths: -------------- apollo/trunk/src/java/apollo/main/Version.java Modified: apollo/trunk/src/java/apollo/main/Version.java =================================================================== --- apollo/trunk/src/java/apollo/main/Version.java 2012-10-12 15:24:16 UTC (rev 25274) +++ apollo/trunk/src/java/apollo/main/Version.java 2012-10-12 20:48:34 UTC (rev 25275) @@ -7,7 +7,7 @@ */ public class Version { - public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.4"; + public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.7"; public static String getVersion() { String timestamp = Config.getTimestamp(); if (timestamp == null) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2012-10-12 15:24:34
|
Revision: 25274 http://gmod.svn.sourceforge.net/gmod/?rev=25274&view=rev Author: gk_fan Date: 2012-10-12 15:24:16 +0000 (Fri, 12 Oct 2012) Log Message: ----------- + Fixed bug in AbstractParser for adding analysis to reverse strand. + Fixed WU-BLAST parser to not croak on "Parameters" section (although do people still use WU-BLAST...) Modified Paths: -------------- apollo/trunk/src/java/apollo/dataadapter/analysis/AbstractParser.java apollo/trunk/src/java/apollo/dataadapter/analysis/BlastParser.java Modified: apollo/trunk/src/java/apollo/dataadapter/analysis/AbstractParser.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/analysis/AbstractParser.java 2012-09-07 19:26:44 UTC (rev 25273) +++ apollo/trunk/src/java/apollo/dataadapter/analysis/AbstractParser.java 2012-10-12 15:24:16 UTC (rev 25274) @@ -112,7 +112,7 @@ analyses.getReverseSet()); // PropertyScheme scheme = Config.getPropertyScheme(); for (int i = 0; i < check_analyses.size() && analysis == null; i++) { - FeatureSetI sf = (FeatureSetI) analyses.getFeatureAt(i); + FeatureSetI sf = (FeatureSetI) check_analyses.getFeatureAt(i); String sf_type = sf.getFeatureType(); analysis = ((sf_type.equals(analysis_type)) ? sf : null); Modified: apollo/trunk/src/java/apollo/dataadapter/analysis/BlastParser.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/analysis/BlastParser.java 2012-09-07 19:26:44 UTC (rev 25273) +++ apollo/trunk/src/java/apollo/dataadapter/analysis/BlastParser.java 2012-10-12 15:24:16 UTC (rev 25274) @@ -305,13 +305,13 @@ else if (span != null && found_hit - && line.startsWith ("Query")) { + && line.startsWith ("Query:")) { grabQueryMatch (span, false); } else if (span != null && found_hit - && line.startsWith ("Sbjct")) { + && line.startsWith ("Sbjct:")) { grabSubjMatch (span, false); } // else if (line.startsWith ("Parameters:")) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: Nomi H. <nlh...@lb...> - 2012-09-07 20:29:04
|
unsubscribe |
From: <gk...@us...> - 2012-09-07 19:26:52
|
Revision: 25273 http://gmod.svn.sourceforge.net/gmod/?rev=25273&view=rev Author: gk_fan Date: 2012-09-07 19:26:44 +0000 (Fri, 07 Sep 2012) Log Message: ----------- + Fixed casting issue that was preventing writing to GenBank format Modified Paths: -------------- apollo/trunk/src/java/apollo/dataadapter/genbank/GenbankAdapterGUI.java Modified: apollo/trunk/src/java/apollo/dataadapter/genbank/GenbankAdapterGUI.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/genbank/GenbankAdapterGUI.java 2012-08-31 12:39:45 UTC (rev 25272) +++ apollo/trunk/src/java/apollo/dataadapter/genbank/GenbankAdapterGUI.java 2012-09-07 19:26:44 UTC (rev 25273) @@ -190,7 +190,7 @@ ((GenbankAdapter) driver).setValidationFile (validation_config); } if (((GenbankAdapter) driver).getInput().equals (path)) { - ((GenbankAdapter) driver).commitChanges(((CompositeDataHolder) values).getCurationSet(0), wantTabular); + ((GenbankAdapter) driver).commitChanges((CurationSet)values, wantTabular); } else { logger.warn("Unable to write to " + (wantTabular ? "directory " : "file ")); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2012-04-24 01:14:41
|
Revision: 25265 http://gmod.svn.sourceforge.net/gmod/?rev=25265&view=rev Author: gk_fan Date: 2012-04-24 01:14:29 +0000 (Tue, 24 Apr 2012) Log Message: ----------- Fixed bug that caused crashing when adding transcript to a gene when EDE was open. Modified Paths: -------------- apollo/trunk/src/java/apollo/gui/detailviewers/exonviewer/BaseFineEditor.java Modified: apollo/trunk/src/java/apollo/gui/detailviewers/exonviewer/BaseFineEditor.java =================================================================== --- apollo/trunk/src/java/apollo/gui/detailviewers/exonviewer/BaseFineEditor.java 2012-04-06 18:05:19 UTC (rev 25264) +++ apollo/trunk/src/java/apollo/gui/detailviewers/exonviewer/BaseFineEditor.java 2012-04-24 01:14:29 UTC (rev 25265) @@ -182,8 +182,8 @@ AnnotatedFeatureI gene = evt.getChangedAnnot(); int trans_count = gene.size(); for (int i = 0; i < trans_count; ++i) { - Transcript t = (Transcript) gene.getFeatureAt (i); if (evt.isUndo()) { + Transcript t = (Transcript) gene.getFeatureAt (i); //System.out.printf("Attaching %s(%d)\n", t, t.hashCode()); editorPanel.attachAnnot(t); if (currentAnnot != null && t.getName().equals(currentAnnot.getName())) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2011-09-26 09:20:47
|
Revision: 25211 http://gmod.svn.sourceforge.net/gmod/?rev=25211&view=rev Author: gk_fan Date: 2011-09-26 09:20:35 +0000 (Mon, 26 Sep 2011) Log Message: ----------- Added link to MAKER Modified Paths: -------------- apollo/trunk/src/java/apollo/gui/menus/LinksMenu.java Modified: apollo/trunk/src/java/apollo/gui/menus/LinksMenu.java =================================================================== --- apollo/trunk/src/java/apollo/gui/menus/LinksMenu.java 2011-09-23 20:33:38 UTC (rev 25210) +++ apollo/trunk/src/java/apollo/gui/menus/LinksMenu.java 2011-09-26 09:20:35 UTC (rev 25211) @@ -45,6 +45,7 @@ makeLink("tRNAscan-SE (tRNA gene finder)", "http://lowelab.ucsc.edu/tRNAscan-SE/"); makeLink("CMS Molecular Biology Resource", "http://mbcf.dfci.harvard.edu/cmsmbr/"); makeLink("BCM Search Launcher", "http://searchlauncher.bcm.tmc.edu/"); + makeLink("MAKER", "http://www.yandell-lab.org/software/maker.html"); // TODO - introduce a parameter that controls this feature, instead of using global DEBUG (deprecated) // (it should be the same parameter that gets used for apollo.external.IgbBridge) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sco...@us...> - 2011-09-20 17:53:55
|
Revision: 25192 http://gmod.svn.sourceforge.net/gmod/?rev=25192&view=rev Author: scottcain Date: 2011-09-20 17:53:42 +0000 (Tue, 20 Sep 2011) Log Message: ----------- adding an "out of date" message to the apollo readme (it used the triggers version) Modified Paths: -------------- schema/trunk/chado/README.Apollo Modified: schema/trunk/chado/README.Apollo =================================================================== --- schema/trunk/chado/README.Apollo 2011-09-20 03:42:32 UTC (rev 25191) +++ schema/trunk/chado/README.Apollo 2011-09-20 17:53:42 UTC (rev 25192) @@ -1,3 +1,18 @@ +Note that this document is quite old, and while it may still work +this way, it can't be guaranteed. Most people who use Apollo +with Chado do not do it this way anymore and instead use the +adapter that comes with Apollo (sometimes known as the "Crabtree +adapter" after the original author Jonathan Crabtree). For +more information on it, see the Apollo tutorial at the GMOD +website: + + http://gmod.org/wiki/Apollo_Tutorial + +Scott +9/20/2011 + + + This needs to be better documented, but here is a start: In order to use Apollo read/write with chado, here are things that need to This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: vishwas v. <vis...@gm...> - 2011-08-26 18:27:17
|
Hi, I am working at the K-State Bioinformatics Center. Here we have set up a webstart version of Apollo for our website http://agripestbase.org. It is connected to a chado-postgresql database through a chado-adaptor. Whenever we annotate any gene and save it in Apollo, it shows up in GBrowse too as GBrowse is also connected to the same database. But when we delete the same annotated gene from Apollo by right clicking on it. It is deleted from the annotation (blue) track but it is still there in the annotation tab in the menu of Apollo. Also when we see in Gbrowse it is there. From which we concluded that even after deleting the gene from Apollo it is not removed completely from all the tables in the database, hence it shows up again in GBrowse and Apollo annotation tab (in menu) too. We are using ubuntu 10.04, Apollo 1.11.6, Chado 0.30, PostgreSql 8.4, GBrowse 2.23 versions. Please it will be great if any one could let us know if it is a bug in apollo or we have done something wrong. Regards, Vishwas Vaswani Kansas State University |
From: <gk...@us...> - 2011-04-06 19:16:37
|
Revision: 24784 http://gmod.svn.sourceforge.net/gmod/?rev=24784&view=rev Author: gk_fan Date: 2011-04-06 19:16:27 +0000 (Wed, 06 Apr 2011) Log Message: ----------- Added phase to CDS features in GFF3 (as required). Modified Paths: -------------- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2011-04-06 16:00:48 UTC (rev 24783) +++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2011-04-06 19:16:27 UTC (rev 24784) @@ -299,6 +299,7 @@ tStart = tEnd; tEnd = tmp; } + int currentLength = 0; for (Object o : feat.getFeatures()) { SeqFeatureI child = (SeqFeatureI)o; SeqFeatureI cds = null; @@ -322,6 +323,8 @@ cds.setFeatureType("CDS"); cds.setId(cds.getId() + "-cds"); cds.setName(cds.getName() + "-cds"); + cds.setPhase(currentLength % 3); + currentLength += cds.length(); children.add(cds); } } Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java 2011-04-06 16:00:48 UTC (rev 24783) +++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java 2011-04-06 19:16:27 UTC (rev 24784) @@ -568,7 +568,10 @@ end = feat.getHigh(); score = feat.getScore(); strand = feat.getStrand(); - phase = feat.getPhase(); + // phase only applies to CDS + if (type.equals("CDS")) { + setPhase(feat.getPhase()); + } id = feat.getId(); name = feat.getName(); //populate dbxrefs This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2011-03-12 15:49:04
|
Revision: 24641 http://gmod.svn.sourceforge.net/gmod/?rev=24641&view=rev Author: gk_fan Date: 2011-03-12 15:48:49 +0000 (Sat, 12 Mar 2011) Log Message: ----------- Fixed issue with writing polypeptides to Chado when using GmodNameAdapter (id not being auto generated for polypeptides). Modified Paths: -------------- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoWriter.java Modified: apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoWriter.java =================================================================== --- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoWriter.java 2011-03-11 22:07:57 UTC (rev 24640) +++ apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoWriter.java 2011-03-12 15:48:49 UTC (rev 24641) @@ -802,7 +802,7 @@ protected String getChadoPeptideName(ApolloNameAdapterI nameAdapter, String name, SeqFeatureI pfeat) { if (nameAdapter instanceof GmodNameAdapter) { - setChadoUniquename(pfeat); + setChadoUniquename(pfeat, nameAdapter); return pfeat.getId(); } return super.getChadoPeptideName(nameAdapter, name, pfeat); @@ -830,11 +830,22 @@ */ private void setChadoUniquename(SeqFeatureI feat) { + ApolloNameAdapterI nameAdapter = this.adapter.getNameAdapter((AnnotatedFeatureI)feat); + setChadoUniquename(feat, nameAdapter); + } + + /** Sets the Chado uniquename for a feature. Currently only supports GmodNameAdapter + * instances. + * + * @param feat - SeqFeatureI object to have the uniquename set. + */ + private void setChadoUniquename(SeqFeatureI feat, ApolloNameAdapterI nameAdapter) + { if (!feat.isAnnot()) { return; } AnnotatedFeatureI annot = (AnnotatedFeatureI)feat; - ApolloNameAdapterI nameAdapter = this.adapter.getNameAdapter(annot); +// ApolloNameAdapterI nameAdapter = this.adapter.getNameAdapter(annot); String id = annot.getId(); if (nameAdapter instanceof GmodNameAdapter) { GmodNameAdapter gmodNameAdapter = (GmodNameAdapter)nameAdapter; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-11-08 21:57:54
|
Revision: 24104 http://gmod.svn.sourceforge.net/gmod/?rev=24104&view=rev Author: nomi Date: 2010-11-08 21:57:46 +0000 (Mon, 08 Nov 2010) Log Message: ----------- Fixed NIH grant number Modified Paths: -------------- apollo/trunk/doc/html/index.html apollo/trunk/doc/html/userguide.html Modified: apollo/trunk/doc/html/index.html =================================================================== --- apollo/trunk/doc/html/index.html 2010-11-08 18:55:37 UTC (rev 24103) +++ apollo/trunk/doc/html/index.html 2010-11-08 21:57:46 UTC (rev 24104) @@ -68,6 +68,6 @@ <P><HR><P> <P> <font size=2> -This work was supported by NIH grant 1R01GM080203-01 from tne National Institute of General Medical Sciences (NIGMS).</font> +This work was supported by NIH grant 1R01GM080203-03 from tne National Institute of General Medical Sciences (NIGMS).</font> </BODY> </HTML> Modified: apollo/trunk/doc/html/userguide.html =================================================================== --- apollo/trunk/doc/html/userguide.html 2010-11-08 18:55:37 UTC (rev 24103) +++ apollo/trunk/doc/html/userguide.html 2010-11-08 21:57:46 UTC (rev 24104) @@ -177,7 +177,7 @@ It is a Java application that is easy to install and run on Windows, Mac OS X, or any Unix-type system (including Linux). -Apollo is currently supported by NIH grant 1R01GM080203-01 from the National Institute of General Medical Sciences (NIGMS). +Apollo is currently supported by NIH grant 1R01GM080203-03 from the National Institute of General Medical Sciences (NIGMS). </p><p> The current Apollo team is: </p><ul> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <gk...@us...> - 2010-11-01 18:49:26
|
Revision: 24072 http://gmod.svn.sourceforge.net/gmod/?rev=24072&view=rev Author: gk_fan Date: 2010-11-01 18:49:16 +0000 (Mon, 01 Nov 2010) Log Message: ----------- Added configurable option for allowing partial ORFs to be calculated. Modified Paths: -------------- apollo/trunk/src/java/apollo/config/Style.java apollo/trunk/src/java/apollo/datamodel/FeatureSet.java Modified: apollo/trunk/src/java/apollo/config/Style.java =================================================================== --- apollo/trunk/src/java/apollo/config/Style.java 2010-11-01 16:23:16 UTC (rev 24071) +++ apollo/trunk/src/java/apollo/config/Style.java 2010-11-01 18:49:16 UTC (rev 24072) @@ -203,6 +203,8 @@ protected Hashtable parameters = null; private String overlapDefinition; + + private boolean allowPartialORFs = true; public Style(String styleFileString) { logger.debug("Creating new style "+styleFileString); @@ -627,6 +629,8 @@ } geneticCodeNumber = num; } + } else if (key.equalsIgnoreCase("AllowPartialORFs")) { + this.allowPartialORFs = getBoolean(value); } else { // Stick it in as a generic parameter logger.debug("saved unknown parameter from " + styleFile + ": " + key + "=" + value); @@ -2104,5 +2108,13 @@ parameters = new Hashtable(1, 1.0F); return parameters; } + + /** Gets whether partial ORFs are allowed when calculating longest ORF + * + * @return whether partial ORFs are allowed + */ + public boolean isPartialORFsAllowed() { + return allowPartialORFs; + } } Modified: apollo/trunk/src/java/apollo/datamodel/FeatureSet.java =================================================================== --- apollo/trunk/src/java/apollo/datamodel/FeatureSet.java 2010-11-01 16:23:16 UTC (rev 24071) +++ apollo/trunk/src/java/apollo/datamodel/FeatureSet.java 2010-11-01 18:49:16 UTC (rev 24072) @@ -4,6 +4,7 @@ import java.util.*; import javax.swing.JOptionPane; +import apollo.config.Config; import apollo.util.SeqFeatureUtil; import apollo.util.FeatureList; import apollo.util.QuickSort; @@ -829,16 +830,19 @@ /* just in case the 5 prime end is missing see if a longer translation can be obtained without looking for the ATG */ - start_index = 0; - while (start_index < 3) { - String orf = get_ORF(the_mRNA, start_index, -1); - String aa = getTrimmedAA(orf, start_index); - if (aa.length() > longest_peptide.length()) { - setMissing5prime(true); - longest_peptide = aa; - best_start_index = start_index; + // only do this if Apollo is configured to allow partial ORFs + if (Config.getStyle().isPartialORFsAllowed()) { + start_index = 0; + while (start_index < 3) { + String orf = get_ORF(the_mRNA, start_index, -1); + String aa = getTrimmedAA(orf, start_index); + if (aa.length() > longest_peptide.length()) { + setMissing5prime(true); + longest_peptide = aa; + best_start_index = start_index; + } + start_index++; } - start_index++; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-13 21:32:13
|
Revision: 23971 http://gmod.svn.sourceforge.net/gmod/?rev=23971&view=rev Author: nomi Date: 2010-10-13 21:32:05 +0000 (Wed, 13 Oct 2010) Log Message: ----------- fixed FlyBase release 3 link Modified Paths: -------------- apollo/trunk/doc/html/index.html Modified: apollo/trunk/doc/html/index.html =================================================================== --- apollo/trunk/doc/html/index.html 2010-10-13 21:31:55 UTC (rev 23970) +++ apollo/trunk/doc/html/index.html 2010-10-13 21:32:05 UTC (rev 23971) @@ -24,7 +24,7 @@ Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. It was used by the -FlyBase biologists to construct the <a href=/annot/release3.html>Release 3 annotations</a> on the finished +FlyBase biologists to construct the <a href=http://www.fruitfly.org/annot/release3.html>Release 3 annotations</a> on the finished <i>Drosophila melanogaster</i> genome, and is also a primary vehicle for sharing these annotations with the community. The <a href=http://www.gmod.org>Generic Model Organism Database (GMOD) project</a>, which This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-13 21:32:05
|
Revision: 23970 http://gmod.svn.sourceforge.net/gmod/?rev=23970&view=rev Author: nomi Date: 2010-10-13 21:31:55 +0000 (Wed, 13 Oct 2010) Log Message: ----------- Removed reference to apollo-zip.html, since it hasn't existed since version 1.6.5. Modified Paths: -------------- apollo/trunk/doc/html/faq.html Modified: apollo/trunk/doc/html/faq.html =================================================================== --- apollo/trunk/doc/html/faq.html 2010-10-13 19:36:21 UTC (rev 23969) +++ apollo/trunk/doc/html/faq.html 2010-10-13 21:31:55 UTC (rev 23970) @@ -67,7 +67,7 @@ problematic on some varieties of Unix and Mac OS X. If you are on Linux and are having trouble running the installer, try downloading the Linux installer <i>without</i> Java VM (and make sure you have Java version 1.5+ installed - on your computer). If the installer still doesn't work, <a href=/annot/apollo/apollo-zip.html>click here</a> for an alternative way to install Apollo.<P> + on your computer).<P> <B>Q:</B> I am having trouble getting Apollo to run on my 64-bit Linux system. <BR><B>A:</B> See the answer to the previous question. Also, try installing This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-13 00:30:28
|
Revision: 23959 http://gmod.svn.sourceforge.net/gmod/?rev=23959&view=rev Author: nomi Date: 2010-10-13 00:30:19 +0000 (Wed, 13 Oct 2010) Log Message: ----------- For some reason, these weren't in svn. Fixed mailing list links. Added Paths: ----------- apollo/trunk/doc/html/faq.html apollo/trunk/doc/html/index.html Added: apollo/trunk/doc/html/faq.html =================================================================== --- apollo/trunk/doc/html/faq.html (rev 0) +++ apollo/trunk/doc/html/faq.html 2010-10-13 00:30:19 UTC (rev 23959) @@ -0,0 +1,279 @@ +<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"> +<HTML> +<HEAD> +</HEAD> + +<TITLE>Apollo FAQ</TITLE> + +<BODY BGCOLOR=#FFFFFF TEXT=#000000 LINK=#0033CC VLINK=#CC3300 ALINK=#9900CC> + +<H1 ALIGN=CENTER> +Apollo Frequently Asked Questions +</H1> +<H3 ALIGN=CENTER> +(Also see the <a href=userguide.html>Apollo Userguide</a>) +</H3> + +<B>Q:</B> What is Apollo? +<BR><B>A:</B> Apollo is a genome annotation viewer and editor. +<P> +<B>Q:</B> What isn't Apollo? +<BR><B>A:</B> Apollo will not analyze your sequence for you. It will not +directly help you find sequencing errors or SNPs. And it doesn't toast bread. +<P> +<B>Q:</B> Why is it called Apollo? +<BR><B>A:</B> Apollo was the Greek god of the sun, music, poetry, prophecy, +agriculture, and pastoral life. Sounds good to us. Or, at any rate, +better than another possible name for our annotation tool: GOAT (GenOme +Annotation Tool). +<P> +<B>Q:</B> Is Apollo an applet? +<BR><B>A:</B> No, Apollo is a Java application--you can <a +href=install.html>download</a> the software and install it on your +computer and run it locally. +<P>We have recently enabled Apollo to run as a Web start application +(which can be launched from a browser, much like an applet), but we +have not yet made this publicly available due to limitations from +the data server side. +<P> +<B>Q:</B> What platforms does Apollo run on? +<BR><B>A:</B> Windows (98, 2000, XP, etc.), Mac OS X (please note that +Apollo is <b>not</b> intended for use on pre-OS X Macs), and any Unix-type +system (Solaris, Linux, etc.). +<P> +<B>Q:</B> Do I need to install Java on my computer in order to run Apollo? +<BR><B>A:</B> Probably not. If you don't already have Java installed, you can <a +href=install.html>download</a> Apollo packaged with the appropriate Java +Virtual Machine (JVM) for your platform. However, if you are running Mac +OS X, you may need to update your JVM--see the next question. +<P> +<B>Q:</B> What version of Java does Apollo require? +<BR><B>A:</B> JDK1.5+ is required for all platforms. +Please see <a href=http://www.apple.com/softwareupdate>Apple's instructions on downloading the latest JDK (currently 1.6)</a>, using Software Updates. +<P> +<B>Q:</B> How much memory does Apollo need? +<BR><B>A:</B> Apollo uses a lot of memory, largely due to +the sheer size of the annotation data. +In order to use Apollo, your computer will need to have at least 164Mb of +RAM. Moreover, even if you have that much memory, you will probably find that if you try +to run more than one instance of Apollo at the same time, performance +will suffer. Also note that if you load a very +large region, Apollo will use up more memory. Keep in mind that other applications running on your +computer also use memory, so you will get better performance if you shut down other applications (Photoshop, Word, etc.) before you launch Apollo. +<P> + +<B>Q:</B> The installer is not working for me. +<BR><B>A:</B> The installer software (a third-party product) has been +problematic on some varieties of Unix and Mac OS X. +If you are on Linux and are having trouble running the installer, try downloading the Linux installer +<i>without</i> Java VM (and make sure you have Java version 1.5+ installed + on your computer). If the installer still doesn't work, <a href=/annot/apollo/apollo-zip.html>click here</a> for an alternative way to install Apollo.<P> + +<B>Q:</B> I am having trouble getting Apollo to run on my 64-bit Linux system. +<BR><B>A:</B> See the answer to the previous question. Also, try installing +a different Java Virtual Machine. One 64-bit Linux user reported trouble using Red Hat's Java, and was +only able to get Apollo to work when he used Sun's Java. +<P> + +<B>Q:</B> I am having trouble getting Apollo to run on my Mac--the Apollo icon +bounces a few times, but Apollo does not come up. +<BR><B>A:</B> Some security-related software updates on Panther (v10.3) interfere +with Java and prevent Apollo from launching from the shortcut. We are looking into +how to address that, but there are two workarounds: +<BR> +<LI> Upgrade your Mac to Tiger (10.4) or later (Leopard or Snow Leopard); or<BR> +<LI> Launch Apollo from the command line. First, start a Terminal window (Applications -> Utilities -> Terminal). In the Terminal window, cd to the directory where you installed Apollo, usually /Applications/Apollo, and type ./bin/apollo (note the lowercase a):<BR> +<pre><dd>cd /Applications/Apollo +<dd>./bin/apollo</pre> +</dd> +You will see the text output from Apollo in the Terminal window, and an Apollo +window should come up. +<P> +<B>Q:</B> I want to see the text output from Apollo on my Mac running Tiger. I opened a Console window, as it says in the userguide, but I don't see output there. +<BR><B>A:</B> Something in Tiger has stopped this from working. We are investigating this. For now, you can see the text output by launching Apollo from a Terminal window (see the previous question) rather than by clicking on the icon. + +<P> +<B>Q:</B> Is there an Apollo mailing list? +<BR><B>A:</B> Yes; you can <a +href=https://lists.lbl.gov/sympa/info/apollo>subscribe here</a>. +In order to reduce spam, only members can send messages to the list. +This mailing list has low traffic and is not used for any purpose other than +Apollo updates and questions. (If you receive spam that appears to be from +the apollo mailing list, it is not really--the address is forged.) +<P> +<B>Q:</B> What data formats does Apollo read? +<BR><B>A:</B>The most robust Apollo data adapters read <a href=game.rng.txt>GAME XML</a> (the format used for the +Drosophila annotations), ChadoXML (the version used at FlyBase Harvard) and the <a +href=http://www.sanger.ac.uk/Software/formats/GFF/>Ensembl version of +GFF</a>. The <a href=http://www.ensembl.org>Ensembl</a> group has enabled Apollo to read data +via the Ensembl CGI and directly from Ensembl databases, with the EnsJ/Otter +adapter. +<P> +There are also two useful data adapters currently under development. +The Analysis adapter lets you read raw analysis results (BLAST, sim4, +GENSCAN, etc.) into Apollo. This is mostly working, although the GUI +needs work. The GenBank adapter is also mostly working but needs +more testing. +<P> +New in Release 1.5.0 is a Chado XML adapter. Right now, it is very +FlyBase-specific and needs to be generalized, but it would be a good starting +point for a group that is using a Chado database. +<P> We recently did some preliminary work towards enabling Apollo to act +as a client for <a target=_new href=http://biodas.org/documents/das2/das2_protocol.html>DAS/2</a> servers. It can now read simple DAS2XML files. +<P> +<B>Q:</B> Is there a schema for GAME XML? +<BR><B>A:</B>Yes, <a href=game.rng.txt>game.rng</a>. If you find a +game.dtd, please disregard it--it was not a good schema description for GAME XML. +For more about the GAME schema, please see doc/schema-notes in the Apollo +distribution. +<P> +<B>Q:</B> Apollo is not working for me--I tried to get Drosophila +melanogaster data and got the error message "Can't connect to URL--server not responding." +<BR><B>A:</B>This is not an Apollo problem--this is a problem with the +FlyBase server that supplies the D. melanogaster annotation data. The server +or the database it accesses may be down, or the traffic may be too heavy. +<P> +Another possible issue is that you might have a firewall that prevents the data from getting to +your computer. If you use a proxy, be sure to set the proxy by clicking the "Proxy settings" +button before trying to load data. +<P> +<B>Q:</B> How can I download and run the latest in-development version +of Apollo? +<BR><B>A:</B> +Keep in mind that if you try to run the very latest Apollo, there are no +guarantees that it will work correctly. We are actively developing it, +and often there are many bugs that crop up between releases and then are +fixed. So on any given day, it's possible that the up-to-the-minute +Apollo won't run at all (though that is rare) or that various aspects of +it will be broken. +<P> +Occasionally, someone will check in code that doesn't compile; when this +happens, it's always fixed quickly (within a day). But if you get lots +and lots of errors when you try to make, there's probably something wrong +with your environment (not having APOLLO_ROOT set properly is the most +common mistake). +<P> +Here is the command I use for checking out the whole Apollo +distribution from sourceforge: +<pre> +setenv CVS_RSH ssh +cvs -z3 -d:ext:mya...@gm...:/cvsroot/gmod checkout -d apollo apollo +</pre> +For "myaccount", substitute your own SourceForge account name. (It's a good +idea to get a SourceForge account if you're going to be doing this--it's +quick, free, and they don't send you spam.) If you don't want to get an +account on SourceForge, you can do an anonymous checkout; however, +anonymous checkouts give you a version that's a few days out of date. +To check out an anonymous version: +<pre> +cvs -d:pserver:ano...@gm...:/cvsroot/gmod login +cvs -d:pserver:ano...@gm...:/cvsroot/gmod checkout -d apollo apollo +</pre> +<P> +The "-d apollo" specifies the directory name you want the Apollo stuff to +go in, so you can change that if you want to put it somewhere else. +<P> +After you've checked out the code, compiling it is straightforward: +<pre> + cd apollo + setenv APOLLO_ROOT `pwd` + cd src/java + make clean [only necessary if you've already compiled and then updated] + make jar +</pre> +You can also use <a target=ant href=http://ant.apache.org/>Ant</a> to +compile the source.<P> +To run your newly compiled apollo: +<pre> + ~/apollo/bin/apollo +</pre> +(where ~/apollo is the directory where you've installed apollo--change +as appropriate). +<P> +Note that all my instructions assume that you're on a Unix-y system +(which includes Macs). +If you're on Windows, I have no idea what to do. I've never tried to +compile on Windows, nor to run anything other than the installed version +of Apollo. I gather you can use Ant to compile on Windows. +<P> +<B>Q:</B> Can I customize Apollo for my own use? +<BR><B>A:</B> Yes. There are many user-customizable options; see the <a +href=userguide.html#configuration>user guide</a> for more information. +<BR> +If you are a Java developer and wish to customize the Apollo code (for +example, by adding a new data adapter to read a different data format), +you can download the source from <a +href=http://www.sourceforge.net/projects/gmod/>SourceForge</a> (see +instructions above). +<P> +<B>Q:</B> Where can I find Apollo developer documentation? +<BR><B>A:</B> +Although Apollo has extensive user documentation, +the documentation for developers is more spotty. +You can look at the <a target=_new href=javadoc/>javadocs</a>, +which are a bit sparse but might still be helpful. If you are +interested in data adapters, look at the data adapter "cookbook" +(<a href=dataadapter_cookbook.html>doc/html/dataadapter_cookbook.html</a>). +Also, the <a href=http://genomebiology.com/2002/3/12/research/0082 target=_paper>Genome Biology +paper about Apollo</a> has a diagram and discussion of the Apollo architecture. +<P> +<B>Q:</B> I would like to annotate the <a href=http://www.lpzoo.com/tour/factsheets/mammals/naked_mole_rat.html>naked mole rat</a> genome using +Apollo. What do I need to do? +<BR><B>A:</B> Well, first you need to run some sequence analysis tools +(such as <a href=http://www.ncbi.nlm.nih.gov/BLAST/>BLAST</a>, <a href=http://genes.mit.edu/GENSCAN.html>GENSCAN</a>, etc.) on your sequence data. We are currently developing +a raw analysis results output loader that can load BLAST results and some +other output formats. +<P> +The only data formats that fully support editing right now are <a href=game.rng.txt>GAME XML</a> +and Chado XML +(<a href=example.xml>Here</a> is an example of annotations and results stored in GAME XML format.) +<P> +At the BDGP, we run sequences through an analysis pipeline that finishes +with a program called BOP, which parses the output from the various +analysis programs and does some filtering and then saves the results as +GAME XML. BOP is now part of the Apollo codebase--however, BOP has not been debugged +and robustified the way Apollo has, so you'll be navigating rougher +terrain if you try to use it. If you've checked out the +Apollo code from SourceForge, you can run BOP from the command line by using the bin/apollo +shell script with the "-bop" option. BOP is also used in the +Analysis Adapter, which lets you read raw analysis results (BLAST, sim4, +GENSCAN, etc.) into Apollo. We are still debugging this. + +<P> +<B>Q:</B> Can I add annotations to the human genome using Apollo? +<BR><B>A:</B> At the moment, the interface to the <a href=http://www.ensembl.org/Homo_sapiens/>human genome +annotations</a> at <a href=http://www.ensembl.org/>Ensembl</a> is +read-only: you can view the annotations but you can't edit them or add +new annotations. We hope to provide that capability soon. +<P>You can, however, edit the Drosophila annotations (or any other +annotations that are stored in GAME XML or Chado XML format, or in +a Chado database). If you wish to submit corrections to our Drosophila +annotations, you can do so at <A +HREF=http://flybase.org/cgi-bin/mailto-fbhelp.html>http://flybase.org/cgi-bin/mailto-fbhelp.html</a>. +<P> +<B>Q:</B> I found a bug in Apollo. +<BR><B>A:</B> We are shocked and horrified; Apollo is 100% bug-free. +Well, ok, that's completely untrue. You can report your bug using the <a href=http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763> +SourceForge Apollo bug tracker</a>. +Please be as specific as possible when you +report bugs--tell us what dataset you were looking at, what operating system +you're on (e.g. Mac OS X), and what you did that caused the bug. Also send us the +output from the Java console (see <a href=userguide.html#stdout>the userguide</a> for instructions +on accessing the console). +Be sure to include your email address so we can contact you for more information about the +bug and notify you when we fix it. +<BR> +We periodically (every month or two) release a new and improved version of Apollo; +visit the <a href=install.html>download page</a> to get the latest version. +<P> +<B>Q:</B> I have made some changes to Apollo that I would like to commit +to the main codebase. +<BR><B>A:</B> We are happy to look at bug fixes and new additions made by +members of the community, and in fact have already incorporated several of +these. Please send your proposed changes to the Apollo mailing list (include any +classfiles or other files that have changed, as well as a description of +what you've changed) and we will review your changes and, if they seem good, +incorporate them into the codebase. (Before sending your changes, please +do a cvs update to make sure your version of apollo is completely up to date.) +</BODY> +</HTML> Added: apollo/trunk/doc/html/index.html =================================================================== --- apollo/trunk/doc/html/index.html (rev 0) +++ apollo/trunk/doc/html/index.html 2010-10-13 00:30:19 UTC (rev 23959) @@ -0,0 +1,73 @@ +<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"> +<HTML> +<link REL="SHORTCUT ICON" href="/favicon.ico"> +<HEAD> +<BASEFONT FACE="Geneva,Arial,Helvetica" SIZE=3> +</HEAD> + +<TITLE>Apollo Genome Annotation Curation Tool</TITLE> + +<BODY BGCOLOR=#FFFFFF TEXT=#000000 LINK=#0033CC VLINK=#CC3300 ALINK=#9900CC> + +<CENTER> +<!-- <IMG SRC="/pics/apollosplash.gerry.jpg" BORDER=0 width=529 height=240 hspace=5 vspace=5 ALT="APOLLO"> --> +<H1>Apollo Genome Annotation Curation Tool</H1> +<IMG SRC="images/cropped-mainwindow-for-web.gif" BORDER=0 width=499 height=274 hspace=5 vspace=5 ALT="APOLLO"> +</CENTER> + +<P> +Apollo is a genome annotation viewer and editor. It was +developed as a collaboration between the <a href=/>Berkeley Drosophila Genome +Project</a> (part of the <a +href=http://flybase.bio.indiana.edu/>FlyBase</a> consortium) and <a href=http://www.ensembl.org>The Sanger Institute</a> in +Cambridge, UK. +Apollo allows researchers to explore genomic +annotations at many levels of detail, and to perform expert annotation +curation, all in a graphical environment. It was used by the +FlyBase biologists to construct the <a href=/annot/release3.html>Release 3 annotations</a> on the finished +<i>Drosophila melanogaster</i> genome, and is also a primary vehicle +for sharing these annotations with the community. +The <a href=http://www.gmod.org>Generic Model Organism Database (GMOD) project</a>, which +aims to provide a complete ready-to-use toolkit for analyzing whole +genomes, has adopted Apollo as its annotation workbench. +Apollo is a Java +application that can be downloaded and run on Windows, Mac OS X, or any Unix-type system +(including Linux). + +<P><HR><P> + +<UL> +<LI> <a href="install.html">Download Apollo</a> (Version 1.11.6, last updated May, 2010) +<P> +<LI> How to cite Apollo:<br> +<a href=http://genomebiology.com/2002/3/12/research/0082 target=_paper> +Apollo: a sequence annotation editor</a>. +Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, +Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, +Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, +Mungall CJ, Clamp ME (2002). +<a href=http://genomebiology.com/><i>Genome Biology</i></a> 2002, 3(12):research0082 +<P> +<LI> Frequently Asked Questions <a href="faq.html">(FAQ)</a> +<P> +<LI> <a href="userguide.html">Apollo userguide</a> (also included when you +download Apollo) +<P> +<LI> <a href=https://lists.lbl.gov/sympa/info/apollo>Subscribe to +the apollo mailing list</a> +<P> +<LI> If you are a developer, you may wish to <a target=_sf +href=http://sourceforge.net/project/showfiles.php?group_id=27707>download the Apollo source +from SourceForge</a>.<BR> +Like many <a href=http://www.gmod.org/>GMOD</a> components, Apollo is distributed under the terms of the +<a href=http://www.opensource.org/licenses/artistic-license.php>Artistic +License</a>.<P> +<LI> For developers: <a target=_sf href=javadoc>Apollo javadocs</a> +</UL> + +<P><HR><P> +<P> +<font size=2> +This work was supported by NIH grant 1R01GM080203-01 from tne National Institute of General Medical Sciences (NIGMS).</font> +</BODY> +</HTML> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-13 00:25:41
|
Revision: 23958 http://gmod.svn.sourceforge.net/gmod/?rev=23958&view=rev Author: nomi Date: 2010-10-13 00:25:31 +0000 (Wed, 13 Oct 2010) Log Message: ----------- Removed links to todos. Fixed text and link to Dolan. Modified Paths: -------------- apollo/trunk/doc/html/userguide.html Modified: apollo/trunk/doc/html/userguide.html =================================================================== --- apollo/trunk/doc/html/userguide.html 2010-10-12 21:38:30 UTC (rev 23957) +++ apollo/trunk/doc/html/userguide.html 2010-10-13 00:25:31 UTC (rev 23958) @@ -260,7 +260,7 @@ <p> Apollo is a Java application that you can download and run on your computer (Windows, Linux, or Mac OS X--earlier Mac versions are not -supported). You can get Apollo <a href="/">here</a>. +supported). You can get Apollo <a href="/current/">here</a>. When you install Apollo, a JVM is bundled with it, unless you are on Mac OS X. </p><h3>Getting the appropriate Java on a Mac</h3> @@ -430,10 +430,9 @@ non-FlyBase data. Also, it cannot yet handle macros, and it doesn't yet deal with some types of "non-Apollo" data such as feature_cvterms. Theoretically, you can use Apollo as a converter between Chado XML and GAME, but we are still -debugging that conversion. Please see <a target="todo" href="http://apollo.berkeleybop.org/todo">doc/todo</a> -for a list of known issues with the Chado XML adapter. +debugging that conversion. </p><p> -The <a href="/game.rng.txt">GAME XML</a> adapter +The <a href="/current/game.rng.txt">GAME XML</a> adapter was written to handle Drosophila data in the older GAME XML format. You should be able to use it to read other types of annotation data in GAME XML format, but you will need to change the tiers file. @@ -458,11 +457,11 @@ gene name (if you selected type gene) or scaffold ID (if you selected golden_path_region). An example of a fruitfly gene is "cact". An example scaffold ID is AE003603. </p><p> -The Chado adapter has known bugs that are described in -<a target="todo" href="http://apollo.berkeleybop.org/chado/chado-jdbc-todo">doc/chado/chado-jdbc-todo</a>. For example, +The Chado adapter has known bugs. +For example, if you request a region that doesn't exist, Apollo will seize up. Also the dashed contig result lines that are present from -the GAME Adapter are not coming up yet. See chado-jdbc-todo for the full listing. +the GAME Adapter are not coming up yet. </p><p> Also, if you ask the server for data by chromosome region (e.g., 2L:10000-20000), you may get an entire scaffold that includes the requested @@ -2033,7 +2032,7 @@ "Edit->Removed gapped columns" will remove the gapped columns (all dashes). So this will remove the gaps of the intron, but the genomic sequence of the intron remains. -On our <a target="todo" href="http://apollo.berkeleybop.org/todo">todo list</a> is adding a menu item to remove the whole intron, +On our todo list is adding a menu item to remove the whole intron, gaps and genomic. </p><p> Columns can be selected/deselected by clicking above the sequences. A red square @@ -2086,11 +2085,7 @@ </p><p> Also be aware that Jalview uses a lot of memory, and that if you launch multiple Jalview windows, Apollo may run out of memory. -</p><p> -Known Jalview bugs are listed in the <a target="todo" href="http://apollo.berkeleybop.org/todo">doc/todo</a> file. -If you encounter a problem that is not listed in that file, please report it via -the <a href="http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763"> -SourceForge Apollo bug tracker</a> or via the <a href="#mailing">Apollo mailing list</a>. +</p> </p><h3><a name="Graphs"></a>Viewing graph data</h3> <p> @@ -2213,7 +2208,7 @@ a genome, you may be interested in using Apollo as a curation tool. This section explains how to use Apollo's annotation curation and editing capabilities. <p> -If you want to edit annotations, Chado XML or <a href="/game.rng.txt">GAME XML</a> format works the best. Ensembl GFF format +If you want to edit annotations, Chado XML or <a href="/current/game.rng.txt">GAME XML</a> format works the best. Ensembl GFF format (which is also used by the Ensembl server) is not a rich enough data format to use for curating annotations. If you turn on editing in gff.style, you will find that it doesn't work right. @@ -2247,7 +2242,7 @@ save GAME 1.0; true means save GAME 1.1). </p><p> Apollo supports several output formats, including <a href="http://www.sanger.ac.uk/Software/formats/GFF/">Ensembl GFF</a> -format and <a href="/game.rng.txt">GAME XML</a>. The GFF format is simpler (though less rich) +format and <a href="/current/game.rng.txt">GAME XML</a>. The GFF format is simpler (though less rich) and more compact. It is a good format for representing simple computational results, but is not the best choice for saving annotations. </p><p> @@ -4107,8 +4102,7 @@ apollo (though they are not by chado). These do not show up as features in the main window, rather they show up as sequence errors in the exon detail editor, with a base pair turned orange. The main window just -displays an orange vertical line for these. <br> - </p> +displays an orange vertical line for these.</p> <p>Select your database from the pull-down menu next to Chado Database. Then select a region to display. The list for Type of Region includes @@ -4131,9 +4125,10 @@ </p><h3>Contributed Apollo Documentation</h3> <a name="Contributed"></a> -<h4>DNA Learning Center at Gramene</h4> -There is a series of Quicktime recordings about using Apollo at <a href="http://www.dnalc.org/gramene/clips/">Gramene</a>. -<p> +<h4>DNA Learning Center</h4> +<p>The Dolan DNA Learning Center at Cold Spring Harbor Laboratory uses Apollo to teach students how to annotate genomes. +Visit the <a target="_new" href="http://www.dynamicgene.org/annotation/annotation.html">Dynamic Gene</a> annotation page +to check it out!</p> </p><h2>Acknowledgements</h2> <a name="acknowledgements"></a> @@ -4141,7 +4136,7 @@ <p></p><hr><p> <!-- hhmts start --> -Last modified: Tue Oct 12 14:00:27 PDT 2010 +Tue Oct 12 17:06:37 PDT 2010 <!-- hhmts end --> </p></output></li></body></html> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-12 21:39:38
|
Revision: 23957 http://gmod.svn.sourceforge.net/gmod/?rev=23957&view=rev Author: nomi Date: 2010-10-12 21:38:30 +0000 (Tue, 12 Oct 2010) Log Message: ----------- Changed reference to nonexistent image apollosplash.jpg back to apollosplash.gerry.jpg. Modified Paths: -------------- apollo/trunk/doc/html/userguide.html Modified: apollo/trunk/doc/html/userguide.html =================================================================== --- apollo/trunk/doc/html/userguide.html 2010-10-12 21:03:56 UTC (rev 23956) +++ apollo/trunk/doc/html/userguide.html 2010-10-12 21:38:30 UTC (rev 23957) @@ -7,7 +7,7 @@ <h1 align="center">Apollo User Guide </h1> -<center><img src="images/apollosplash.jpg" height="240" width="529"> +<center><img src="images/apollosplash.gerry.jpg" width="529"> <h2>Version 1.11.x<br>October 2009</h2> </center> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-12 21:04:04
|
Revision: 23956 http://gmod.svn.sourceforge.net/gmod/?rev=23956&view=rev Author: nomi Date: 2010-10-12 21:03:56 +0000 (Tue, 12 Oct 2010) Log Message: ----------- Updated the Apollo mailing list URL and a few other hardcoded URLs. Modified Paths: -------------- apollo/trunk/doc/html/dataadapter_cookbook.html apollo/trunk/doc/html/tiers.html Modified: apollo/trunk/doc/html/dataadapter_cookbook.html =================================================================== --- apollo/trunk/doc/html/dataadapter_cookbook.html 2010-10-12 21:03:18 UTC (rev 23955) +++ apollo/trunk/doc/html/dataadapter_cookbook.html 2010-10-12 21:03:56 UTC (rev 23956) @@ -1388,7 +1388,7 @@ this adapter, but until we get to that point, theres no urgency to finely configure this. So in other words if you are wanting to connect up your chado database, please contact us -via the <a target=_new href=http://mail.fruitfly.org/mailman/listinfo/apollo>Apollo mailing list</a> +via the <a target=_new href=https://lists.lbl.gov/sympa/info/apollo>Apollo mailing list</a> and we can discuss what your chado database looks like, how much it conforms to SO, and figure out where the fine grain configging will need to @@ -1479,7 +1479,7 @@ </p> <p></p> <dd><i>Note: Lincoln's notes were written before the <a - href="http://www.fruitfly.org/annot/apollo/game.rng.txt">RNG schema</a> + href="/game.rng.txt">RNG schema</a> for GAME XML was written to replace the inaccurate DTD.</i> <p><seq><br> id yes<br> Modified: apollo/trunk/doc/html/tiers.html =================================================================== --- apollo/trunk/doc/html/tiers.html 2010-10-12 21:03:18 UTC (rev 23955) +++ apollo/trunk/doc/html/tiers.html 2010-10-12 21:03:56 UTC (rev 23956) @@ -16,7 +16,7 @@ etc.). <P> There is a good description of the Apollo tiers files in the -<a href=http://www.fruitfly.org/annot/apollo/userguide.html#TiersFiles>Apollo user +<a href=/userguide.html#TiersFiles>Apollo user manual</a>--please read that section before you read this description of how to create and change tiers files. <P>If you edit the tiers file, be aware that each tier line and each type line must be a @@ -29,7 +29,7 @@ <br> <h3>Adding new types to a tiers file</h3> Sometimes when you display a datafile, you will see messages in the -<a href=http://www.fruitfly.org/annot/apollo/userguide.html#stdout>Apollo console</a> +<a href=/userguide.html#stdout>Apollo console</a> about new feature property schemes being created, e.g. <P> Creating new feature property scheme for Gene Prediction<br> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-12 21:03:28
|
Revision: 23955 http://gmod.svn.sourceforge.net/gmod/?rev=23955&view=rev Author: nomi Date: 2010-10-12 21:03:18 +0000 (Tue, 12 Oct 2010) Log Message: ----------- Really just ../game.rng, but used by userguide.html. Added Paths: ----------- apollo/trunk/doc/html/game.rng.txt Added: apollo/trunk/doc/html/game.rng.txt =================================================================== --- apollo/trunk/doc/html/game.rng.txt (rev 0) +++ apollo/trunk/doc/html/game.rng.txt 2010-10-12 21:03:18 UTC (rev 23955) @@ -0,0 +1,844 @@ +<?xml version="1.0"?> +<grammar ns="" xmlns="http://relaxng.org/ns/structure/1.0" datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> + <!-- RELAX-NG (see relaxng.org) schema description for GAME XML --> + <!-- The rng file is the home of the GAME XML schema. game.xsd can be + derived from it using trang (see schema-notes), as can game.rnc if you + want the compact format. Therefore, any modifications to the schema + should be made to the rng file first. --> + <!-- Schema for GAME XML, v1.0. + Note that this schema is liberal--it is possible to construct GAME XML + files that Apollo's GAME XML parser doesn't like but yet are + validated by this schema. + Started by Sohel Merchant at RGD; edited and commented by Suzanna + Lewis; edited and commented by Andrew Dalke; extensively revised by + Nomi Harris 11/2004 --> + <!-- Note on entities: some XML files include non-standard entities for + representing Greek letters, e.g. &tgr;. Theoretically, all nonstandard + entities should be defined in the XML stream itself. This is not the + case with the Apollo data because Apollo has code to deal with these + entities. It turns out to be non-trivial to make the schema deal with + entities that are nonstandard and not defined in the XML input, so if + you try to validate a GAME XML file that includes these Greek entities, + you will unfortunately get a fatal error. NH, 12/07/2004 --> + <start> + <choice> + <!-- The root element; represents the curation of one or more + sequences of DNA, RNA, or AA. Most commonly, the <game> element + represents the curation of a single sequence. --> + <element name="game"> + <optional> + <attribute name="version"> + <data type="string"/> + </attribute> + </optional> + <oneOrMore> + <choice> + <!-- <seq>: Represents a sequence of DNA, RNA, or AA. There + is generally one <seq> in the document representing the + primary sequence being curated, and other <seq>'s that + support the curation of the primary sequence. The primary + <seq> is directly under the <game> element, and is identified + by having its "focus" attribute set to true. Each <seq> has + one or more <db_xref> to indicate where the seq can be found + using a particular unique identifier. + For Drosophila curation, BDGP uses the primary <seq> to represent + an accession, and other <seq>'s to represent cDNA's, protein + coding sequences, and homologous sequences that are + referenced by computational analyses such as tblastx. --> + <element name="seq"> + <ref name="seqType"/> + </element> + <!-- <map_position>: Maps a sequence onto a chromosome. For + Drosophila curation, only one <map_position> is used per + file, to specify the location of the primary sequence on a + chromosome. --> + <element name="map_position"> + <interleave> + <attribute name="seq"> + <data type="string"/> + </attribute> + <attribute name="type"> + <data type="string"/> + </attribute> + <!-- Theoretically, we should have arm or chromosome, but + not both. In practice, I've sometimes seen both. --> + <optional> + <ref name="arm"/> + </optional> + <optional> + <ref name="chromosome"/> + </optional> + <optional> + <ref name="organism"/> + </optional> + <element name="span"> + <ref name="spanType"/> + </element> + </interleave> + </element> + + <!-- <annotation>: Represents a set of related seqence + features and a collection of genetic information describing + them. The term "sequence feature" means a segment of DNA. + An annotation will generally contain a number of + <feature_set>'s, each of which represents a set of related + sequence features that have a specific location. A + <feature_set> can contain nested <feature_set>'s (although in + practice this has not yet occured), as well as one or more + <feature_span>'s, each of which represents an individual + sequence feature. A <feature_span> can contain <evidence> + which specifies a result id and result type. An <annotation> + can have one or more <db_xref>'s. + For Drosophila curation, the types of annotations are: gene, + pseudogene, transposon, tRNA, rRNA, snRNA, snoRNA, + "misc. non-coding RNA", and "miscellaneous curator's + observation". [Note: there are now some additional types.] + For an <annotation> of type "gene", one <feature_set> element + represents each transcript, and for each transcript, one + <feature_span> element represents each exon. --> + <element name="annotation"> + <interleave> + <optional> + <attribute name="problem"> + <data type="boolean"/> + </attribute> + </optional> + <attribute name="id"> + <data type="NMTOKEN"/> + </attribute> + <ref name="name"/> + <!-- Type should be constrained to be a SO term --> + <ref name="type"/> + <optional> + <element name="date"> + <ref name="dateType"/> + </element> + </optional> + <!-- A lot of magic is held in the property element. + It became the elastic that let us add new data (and have it + be saved to the database) without having to change any of + the other code. To get the full functionality of Apollo + maybe we should enumerate the special types here? --> + <zeroOrMore> + <element name="property"> + <ref name="propertyType"/> + </element> + </zeroOrMore> + <zeroOrMore> + <ref name="synonym"/> + </zeroOrMore> + <optional> + <element name="gene"> + <optional> + <!-- This is another leftover. The idea was that sometimes + a curator might not 'know' which gene it is (from the literature) + but they have a list of suspects that it might be. + Perhaps we should eliminate this entire <gene> element. --> + <attribute name="association"> + <data type="string"/> + </attribute> + </optional> + <attribute name="id"> + <data type="string"/> + </attribute> + <ref name="name"/> + <optional> + <!-- <dbxref>: Represents a database + cross-reference. The <xref_db> is the name of the + database (e.g. EMBL), and the <db_xref_id> is the + unique id within that database. --> + <element name="dbxref"> + <ref name="dbxrefType"/> + </element> + </optional> + </element> + </optional> + <!-- other db xrefs other than the primary one in the gene element --> + <zeroOrMore> + <element name="dbxref"> + <ref name="dbxrefType"/> + </element> + </zeroOrMore> + <zeroOrMore> + <element name="comment"> + <ref name="commentType"/> + </element> + </zeroOrMore> + <optional> + <element name="description"> + <data type="string"/> + </element> + </optional> + <choice> + <oneOrMore> + <!-- <feature_set>: Represents a set of sequence + features (segments of DNA). + For Drosophila curation, a <feature_set> represents a + transcript, and contains a number of <feature_span>'s + which represent the start codon and the exons. Each + <feature_set> typically contains two <seq>'s, one for + the cDNA sequence and one for the protein-coding + sequence of the transcript. --> + <element name="feature_set"> + <ref name="feature_setType"/> + </element> + </oneOrMore> + <oneOrMore> + <!-- <feature_span>: Represents a sequence feature + (segment of DNA), including its location, which is + specified in a <seq_relationship>. Can contain + <evidence> which specifies a result id and result + type. [Actually, I don't think we have explicit + <evidence> tags anymore.] + For Drosophila curation, a <feature_span> represents + an exon or a start codon. Each <feature_span> + contains a <seq_relationship> of type "query" + specifying the location on the primary sequence of + the document, which is typically an accession. --> + <element name="feature_span"> + <ref name="feature_spanType"/> + </element> + </oneOrMore> + <oneOrMore> + <!-- for one level annots just have a seq relationship which just gives + coords for the annot -- new change to game as of fall 2005 --> + <element name="seq_relationship"> + <ref name="seq_relationshipType"/> + </element> + </oneOrMore> + </choice> + </interleave> + </element> + + <!-- <computational_analysis>: Contains evidence from + computational analysis programs such sim4 and blastx. + <result_set>'s and <result_span>'s represent a tree structure + of results, with <result_set>'s representing branch nodes + (e.g. gene matches), and <result_span>'s representing leaf + nodes (e.g. exon matches). The elements <feature_set>, + <feature_span>, <result_set>, <result_span> run parallel to + one another. Both allow multiple levels of nesting, both have + physical location(s) on sequences. The key differences are + that 'features' have results as evidence and results have + some form of an associated score for the assay. + <seq_relationship>'s provides the locations on the underlying + <seq>'s. --> + <element name="computational_analysis"> + <interleave> + <!-- program name is required --> + <ref name="program"/> + <optional> + <ref name="database"/> + </optional> + <!-- version of program used --> + <optional> + <ref name="version"/> + </optional> + <!-- There's not usually a "type" field here, but some + datasets seem to have it. --> + <optional> + <ref name="type"/> + </optional> + <zeroOrMore> + <element name="property"> + <ref name="propertyType"/> + </element> + </zeroOrMore> + <!-- date analysis was run --> + <optional> + <element name="date"> + <ref name="dateType"/> + </element> + </optional> + <choice> + <!-- Normally a computational analysis should have + result sets, but sometimes they're empty. --> + <zeroOrMore> + <element name="result_set"> + <ref name="result_setType"/> + </element> + </zeroOrMore> + <!-- some analyses just give single intervals, for example + tRNAscan-SE. Although I will admit that most of the time + what the DB has provided is a 'set' with only a single + 'span' contained within it. --> + <zeroOrMore> + <element name="result_span"> + <ref name="result_spanType"/> + </element> + </zeroOrMore> + </choice> + </interleave> + </element> + <element name="transaction"> + <interleave> + <element name="date"> + <ref name="dateType"/> + </element> + <ref name="author"/> + <ref name="object_class"/> + <ref name="operation"/> + <element name="before"> + <interleave> + <optional> + <ref name="annotation_id"/> + </optional> + <optional> + <ref name="id"/> + </optional> + <optional> + <ref name="transcript_name"/> + </optional> + <optional> + <ref name="name"/> + </optional> + </interleave> + </element> + <element name="after"> + <interleave> + <optional> + <ref name="annotation_id"/> + </optional> + <optional> + <ref name="id"/> + </optional> + <optional> + <ref name="transcript_name"/> + </optional> + <optional> + <ref name="name"/> + </optional> + </interleave> + </element> + </interleave> + </element> + <!-- Obsolete types of transaction record, + included for backwards compatibility --> + <element name="deleted_transcript"> + <attribute name="id"> + <data type="string"/> + </attribute> + </element> + <element name="changed_gene"> + <attribute name="id"> + <data type="string"/> + </attribute> + </element> + </choice> + </oneOrMore> + </element> + <ref name="transcript_name"/> + <ref name="start"/> + <ref name="end"/> + <ref name="position"/> + <ref name="base"/> + <ref name="person"/> + <ref name="alignment"/> + <ref name="operation"/> + <ref name="chromosome"/> + <ref name="score"/> + <ref name="residues"/> + <ref name="xref_db"/> + <ref name="name"/> + <ref name="value"/> + <ref name="annotation_id"/> + <ref name="type"/> + <ref name="organism"/> + <ref name="version"/> + <ref name="arm"/> + <ref name="synonym"/> + <ref name="text"/> + <ref name="description"/> + <ref name="db_xref_id"/> + <ref name="database"/> + <ref name="program"/> + <ref name="author"/> + <ref name="object_class"/> + </choice> + </start> + <define name="position"> + <element name="position"> + <ref name="int"/> + </element> + </define> + <define name="base"> + <element name="base"> + <data type="string"/> + </element> + </define> + <define name="organism"> + <element name="organism"> + <data type="string"/> + </element> + </define> + <define name="result_spanType"> + <interleave> + <optional> + <attribute name="id"> + <data type="string"/> + </attribute> + </optional> + <optional> + <ref name="name"/> + </optional> + <optional> + <ref name="type"/> + </optional> + <optional> + <ref name="score"/> + </optional> + <zeroOrMore> + <element name="output"> + <ref name="outputType"/> + </element> + </zeroOrMore> + <oneOrMore> + <!-- <seq_relationship>: Provides the locations on the underlying + <seq>'s. Every <seq_relationship> absolutely requires a seq_id + reference. There are no hidden assumptions regarding which + sequence the positions refer to - it is firmly explicit. This + makes it possible, among other things, to have the same feature + appear on multiple sequences. --> + <element name="seq_relationship"> + <ref name="seq_relationshipType"/> + </element> + </oneOrMore> + </interleave> + </define> + <!-- Note that some values should really be restricted to a particular + type. For example, sometimes scores appear as type=score, value=12345, + and we'd want to reject value=FOO, but we can't constrain value like + that because in other cases it represents other types of data. --> + <define name="value"> + <element name="value"> + <data type="string"/> + </element> + </define> + <define name="version"> + <element name="version"> + <data type="string"/> + </element> + </define> + <define name="id"> + <element name="id"> + <data type="string"/> + </element> + </define> + <define name="annotation_id"> + <element name="annotation_id"> + <data type="string"/> + </element> + </define> + <define name="type"> + <element name="type"> + <data type="string"/> + </element> + </define> + <define name="outputType"> + <interleave> + <ref name="type"/> + <ref name="value"/> + </interleave> + </define> + <define name="spanType"> + <interleave> + <ref name="start"/> + <ref name="end"/> + </interleave> + </define> + <define name="arm"> + <element name="arm"> + <data type="string"/> + </element> + </define> + <define name="int"> + <data type="int"/> + </define> + <define name="text"> + <element name="text"> + <data type="string"/> + </element> + </define> + <define name="synonym"> + <element name="synonym"> + <data type="string"/> + </element> + </define> + <define name="dbxrefType"> + <interleave> + <ref name="xref_db"/> + <ref name="db_xref_id"/> + </interleave> + </define> + <define name="author"> + <element name="author"> + <data type="string"/> + </element> + </define> + <define name="object_class"> + <element name="object_class"> + <data type="string"/> + </element> + </define> + <define name="database"> + <element name="database"> + <data type="string"/> + </element> + </define> + <define name="feature_spanType"> + <interleave> + <optional> + <attribute name="produces_seq"> + <data type="string"/> + </attribute> + </optional> + <optional> + <attribute name="type"> + <data type="string"/> + </attribute> + </optional> + <optional> + <attribute name="id"> + <data type="NMTOKEN"/> + </attribute> + </optional> + <optional> + <ref name="name"/> + </optional> + <optional> + <ref name="type"/> + </optional> + <oneOrMore> + <element name="seq_relationship"> + <ref name="seq_relationshipType"/> + </element> + </oneOrMore> + </interleave> + </define> + <define name="program"> + <element name="program"> + <data type="string"/> + </element> + </define> + <define name="description"> + <element name="description"> + <data type="string"/> + </element> + </define> + <define name="commentType"> + <interleave> + <optional> + <attribute name="internal"> + <choice> + <value type="NMTOKEN">true</value> + <value type="NMTOKEN">false</value> + </choice> + </attribute> + </optional> + <!-- In some dbs (Otter/Ensembl), comments can have ids --> + <optional> + <attribute name="id"> + <data type="NMTOKEN"/> + </attribute> + </optional> + <ref name="text"/> + <optional> + <ref name="person"/> + </optional> + <optional> + <element name="date"> + <ref name="dateType"/> + </element> + </optional> + <optional> + <!-- Not standard here, but I found it in at least one dataset. --> + <element name="internal"> + <data type="boolean"/> + </element> + </optional> + </interleave> + </define> + <define name="chromosome"> + <element name="chromosome"> + <data type="string"/> + </element> + </define> + <define name="seq"> + <element name="seq"> + <ref name="seqType"/> + </element> + </define> + <define name="feature_setType"> + <interleave> + <optional> + <attribute name="id"> + <data type="NMTOKEN"/> + </attribute> + </optional> + <optional> + <attribute name="problem"> + <data type="boolean"/> + </attribute> + </optional> + <optional> + <attribute name="produces_seq"> + <data type="string"/> + </attribute> + </optional> + <optional> + <!-- Type attribute is redundant with type element, but if we + delete it then older GAME files won't validate. --> + <attribute name="type"> + <data type="string"/> + </attribute> + </optional> + <ref name="name"/> + <optional> + <!-- This should really be restricted to be a SO term --> + <ref name="type"/> + </optional> + <optional> + <ref name="author"/> + </optional> + <optional> + <element name="date"> + <ref name="dateType"/> + </element> + </optional> + <zeroOrMore> + <ref name="synonym"/> + </zeroOrMore> + <zeroOrMore> + <element name="comment"> + <ref name="commentType"/> + </element> + </zeroOrMore> + <optional> + <element name="description"> + <data type="string"/> + </element> + </optional> + <zeroOrMore> + <element name="property"> + <ref name="propertyType"/> + </element> + </zeroOrMore> + <choice> + <oneOrMore> + <element name="feature_set"> + <ref name="feature_setType"/> + </element> + </oneOrMore> + <oneOrMore> + <element name="feature_span"> + <ref name="feature_spanType"/> + </element> + </oneOrMore> + </choice> + + <!-- Can have 0 to 2 seqs (can have one for the mRNA and one for + the peptide). When I tried to make it represent that constraint, + though, the translated xsd ended up with two <seq> elements and + some validators don't like that. So I'm letting it allow zero or + more seqs. --> + <zeroOrMore> + <ref name="seq"/> + </zeroOrMore> + </interleave> + </define> + <define name="person"> + <element name="person"> + <data type="string"/> + </element> + </define> + <define name="operation"> + <element name="operation"> + <data type="string"/> + </element> + </define> + <define name="transcript_name"> + <element name="transcript_name"> + <data type="string"/> + </element> + </define> + <define name="seqType"> + <interleave> + <optional> + <attribute name="type"> + <data type="string"/> + </attribute> + </optional> + <optional> + <!-- There should be only one of these in the entire XML document + On the other hand, it strictly speaking is unneeded because + the focus sequence is the reference sequence of the curation --> + <attribute name="focus"> + <data type="boolean"/> + </attribute> + </optional> + <optional> + <attribute name="md5checksum"> + <data type="string"/> + </attribute> + </optional> + <optional> + <attribute name="length"> + <data type="NMTOKEN"/> + </attribute> + </optional> + <attribute name="id"> + <data type="string"/> + </attribute> + <optional> + <attribute name="version"> + <data type="NMTOKEN"/> + </attribute> + </optional> + <interleave> + <ref name="name"/> + <optional> + <ref name="organism"/> + </optional> + <optional> + <element name="potential_sequencing_error"> + <interleave> + <ref name="type"/> + <ref name="position"/> + <optional> + <ref name="base"/> + </optional> + </interleave> + </element> + </optional> + <zeroOrMore> + <element name="dbxref"> + <ref name="dbxrefType"/> + </element> + </zeroOrMore> + <optional> + <ref name="description"/> + </optional> + <optional> + <ref name="residues"/> + </optional> + </interleave> + </interleave> + </define> + <define name="result_setType"> + <interleave> + <optional> + <attribute name="id"> + <data type="string"/> + </attribute> + </optional> + <ref name="name"/> + <optional> + <!-- Normally you would expect to see scores in result_span, not + result_set --> + <element name="score"> + <data type="float"/> + </element> + </optional> + <optional> + <element name="seq_relationship"> + <ref name="seq_relationshipType"/> + </element> + </optional> + <zeroOrMore> + <element name="output"> + <ref name="outputType"/> + </element> + </zeroOrMore> + <zeroOrMore> + <element name="result_set"> + <ref name="result_setType"/> + </element> + </zeroOrMore> + <zeroOrMore> + <element name="result_span"> + <ref name="result_spanType"/> + </element> + </zeroOrMore> + </interleave> + </define> + <define name="propertyType"> + <interleave> + <ref name="type"/> + <ref name="value"/> + </interleave> + </define> + <define name="dateType"> + <interleave> + <attribute name="timestamp"> + <data type="NMTOKEN"/> + </attribute> + <data type="string"/> + </interleave> + </define> + <define name="alignment"> + <element name="alignment"> + <data type="string"/> + </element> + </define> + <define name="seq_relationshipType"> + <interleave> + <attribute name="seq"> + <data type="string"/> + </attribute> + <optional> + <attribute name="type"> + <choice> + <value type="NMTOKEN">query</value> + <value type="NMTOKEN">subject</value> + </choice> + </attribute> + </optional> + <element name="span"> + <ref name="spanType"/> + </element> + <!-- this alignment element is deprecated. it should only + be used if a cigar property element and the corresponding + seq element are unavailble. Either this or the cigar+seq are + needed to drive the alignment viewer. The alignment is the + string parsed out of the BLAST or sim4 output --> + <optional> + <ref name="alignment"/> + </optional> + </interleave> + </define> + <define name="score"> + <element name="score"> + <data type="float"/> + </element> + </define> + <define name="name"> + <element name="name"> + <data type="string"/> + </element> + </define> + <define name="db_xref_id"> + <element name="db_xref_id"> + <data type="string"/> + </element> + </define> + <define name="xref_db"> + <element name="xref_db"> + <data type="string"/> + </element> + </define> + <define name="end"> + <element name="end"> + <ref name="int"/> + </element> + </define> + <define name="start"> + <element name="start"> + <ref name="int"/> + </element> + </define> + <define name="residues"> + <element name="residues"> + <data type="string"/> + </element> + </define> +</grammar> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <no...@us...> - 2010-10-12 21:00:55
|
Revision: 23954 http://gmod.svn.sourceforge.net/gmod/?rev=23954&view=rev Author: nomi Date: 2010-10-12 21:00:47 +0000 (Tue, 12 Oct 2010) Log Message: ----------- Forgot to update "Last modified" date. Modified Paths: -------------- apollo/trunk/doc/html/userguide.html Modified: apollo/trunk/doc/html/userguide.html =================================================================== --- apollo/trunk/doc/html/userguide.html 2010-10-12 21:00:13 UTC (rev 23953) +++ apollo/trunk/doc/html/userguide.html 2010-10-12 21:00:47 UTC (rev 23954) @@ -4141,7 +4141,7 @@ <p></p><hr><p> <!-- hhmts start --> -Last modified: Thu 04 Mar 2010 12:02:01 PM PST +Last modified: Tue Oct 12 14:00:27 PDT 2010 <!-- hhmts end --> </p></output></li></body></html> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |